Viral mechanisms of protein synthesis can be different from the canonical cellular protein synthesis. Many positive strand RNA viruses, which include animal and plant viruses within the Picornavirus-like super-family, do not have their RNA capped and yet they translate efficiently. In the absence of a 5′ cap, a common strategy for the recruitment of ribosomes is via an internal ribosome entry site (IRES). An IRES is an RNA domain upstream of an open reading frame, which recruits the ribosomes internally onto the RNA independently of a 5′ cap structure or ribosomal scanning from the 5′ end. One main feature of an IRES is that when the IRES is placed in the intergenic region of a bicistronic mRNA, the element is capable of mediating translation of the downstream cistron, through internal recruitment of the translation machinery just upstream of the open reading frame. Translation of the downstream cistron is independent of the translation of the first (upstream) cistron. In a true IRES, translation of the downstream cistron is not effected by inclusion of an upstream stem loop structure located at or near the 5′ end of the RNA, which is capable of inhibiting ribosome 5′ end entry.
Based on their structural conformation and factor requirement, three groups of distinctive animal virus IRES elements have been defined. Class I IRES elements are found in the Dicistroviridae family, are compact in structure and are able to initiate translation alone from a non-AUG codon, without any host factors. Class II IRES elements are modeled by Hepatitis C virus. These IRES elements can recruit the 40S ribosome complex alone but they need factors like eIF3 and eIF2/GTP/Met-tRNAi complex to actually finish the initiation. Class III IRES elements are modeled by Encephalomyocarditis virus (EMCV) and Poliovirus. This type of IRES needs the helicase eIF4A, C-terminal region of eIF4G and often some cellular RNA binding proteins referred to as IRES-transacting factors (ITAF) to initiate translation.
All reported plant IRESes are short relative to those observed in animal viruses, have AU-rich sequences and are devoid of stable structure. IRESes in plant viruses are yet to be explored on a large scale. Tobacco etch virus (TEV), a member of the Potyviridae family, the largest group of plant viruses, has been the model system to study IRES-mediated translation in plants. The TEV reported IRES has two pseudoknot-containing domains at its 144 nucleotide 5′ untranslated region needed to promote cap-independent translation. Potato virus Y, a serious disease for potato production worldwide, has a reported 55 nucleotide IRES in its 188 nucleotide 5′ UTR. Plum pox virus, by contrast, has no specific sequence found to be required for its reported IRES function, with upstream AUG and leaky scanning possibly involved in its translation initiation.
Other IRES elements which have been reported within other plant virus families include Tobacco mosaic virus, a prototype of Tobamoviruses, which uses a 75 nucleotide IRES for the expression of its movement protein from the subgenomic RNA. Crucifer-infecting tobamovirus (crTMV) has an IRES located within an intergenic region for the translation of its coat protein. Potato leafroll virus (PLRV), the type species of the genus Polerovirus in the family Luteoviridae, directs internal ribosome entry with a GA rich motif (Jaag at al., 2003, Proc Natl Acad Sci USA, 100, 8939-8944).
However, the IRES activities of most reported plant viruses remain questionable as well as the degree and/or the context in which they sustain efficient translation. The methodology and experimental approaches used to identify the reported plant IRES elements do not allow an unambiguous conclusion of IRES activity. None of the reported plant IRES elements has been shown to sustain strong translation in the presence of an upstream stem loop structure blocking 5′ end ribosome entry.